Going from Scene - Scene seems to mess things up

I had 2 scenes before - Menu & MainGame. The Menu just consisted of a "Play" button, taking the user to the "MainGame". However, after trying to implement a "difficulty" choice on the Menu, certain methods in MainGame seem to be not running at all. The difficulty seems to be working fine however

The main method which is not running is Update from my GameController class

 using UnityEngine;
 using System.Collections;
 using UnityEngine.UI;
 using UnityEngine.SceneManagement;
 
 public class GameController : MonoBehaviour {
 
     public DotArrayController dac;
     protected bool paused = false;
     public Text countdownText;
     private float count = 3;
     private float secondCount = 2;
     private Vector2 oridgePosish;
 
     // Use this for initialization
     void Start () {
         
         dac.enabled = false;
         oridgePosish = dac.transform.position;
         dac.transform.position = new Vector2 (-500, 0);
         countdownText.transform.position = new Vector2 (680, 444);
         //foreach (DotController d in dac.dots) {
         //    d.transform.position = new Vector2 (-500, 0);
         //}
     }
         
     // Update is called once per frame
     void Update () {
 
         Debug.Log (countdownText.text);
 
         if (count > 0) {
             count -= Time.deltaTime;
         } if (count > 2) {
             countdownText.text = "3";
         } else if (count > 1) {
             countdownText.text = "2";
         } else if (count > 0) {
             countdownText.text = "1";
             secondCount -= Time.deltaTime;
         } 
             
          if (count < 0) {
             countdownText.transform.position = new Vector2 (620, 444);
             countdownText.text = "GO";
             enableDac ();
         } 
 
 
 
         if (Input.GetKeyDown (KeyCode.P)) {
             if (paused) {
                 dac.OnPauseGame ();
                 paused = false;
             } else {
                 dac.OnResumeGame ();
                 paused = true;
             }
 
             //if (Time.timeScale == 1) {
             //    Time.timeScale = 0;
             //
             //} else {
             //    Time.timeScale = 1;
             //
             //}
         }
 
     }
 
     public void enableDac(){
         dac.transform.position = oridgePosish;
         dac.enabled = true;
     }
 
 
 }

The only big change is a GlobalControl class I used:

 using UnityEngine;
 using System.Collections;
 
 public class GlobalControl : MonoBehaviour {
 
     public int currentDifficulty;
 
     public static GlobalControl Instance;
 
     void Awake ()
     {
         if (Instance == null) {
             DontDestroyOnLoad (gameObject);
             Instance = this;
         } else if (Instance != this) {
             Destroy (gameObject);
         }
     }
 
     public void savePlayer()
     {
         GlobalControl.Instance.currentDifficulty = currentDifficulty;
     }
 
 }
 
 

Any help would be great, cheers.